|
| Status |
Public on Jun 07, 2023 |
| Title |
Adult intestinal esg+ cells, control batch1, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Adult midgut
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Adult midgut
cell type: esg-positive cells
genotype: esg-Gal4, UAS-GFP, tub-Gal80[ts]
treatment: temperature switch 18>29C
|
| Treatment protocol |
Switched to 29ºC in normal food for 2 days prior to dissection.
|
| Growth protocol |
Flies maintained at 18ºC in normal food until adulthood.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We dissected 100 midguts/genotype in triplicate and for each sample 20,000–40,000 cells were sorted into RNAse-free 1× PBS with 5 mM EDTA. RNA was isolated using the Arcturus PicoPure™ RNA Isolation Kit.
The entire amount of isolated RNA was used as input for RNA-amplification using the Arcturus™ RiboAmp™ HS PLUS Kit. Two hundred nanograms of amplified aRNA was used as input for RNA-Seq library preparation using the TruSeq Stranded mRNA Library Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
1x50bp
|
| Data processing |
map with `--readFilesCommand zcat --outMultimapperOrder Random --outSAMmultNmax 1 --runMode alignReads --outSAMtype BAM Unsorted --quantMode GeneCounts`
index with `bamtools index -in aligned.bam -out indexed.bam`
sort with `bamtools sort -out sorted.bam -in indexed.bam`
count reads per gene with `featureCounts -T 8 -p -C -F GTF -t exon -g gene_id ...`
Assembly: FB2019_03 Dmel Release 6.28
Supplementary files format and content: .featurecounts files contain the mapping of reads to each gene in plain text (tab-delimited)
Supplementary files format and content: .summary files contain summary statistics of the mapping in plain text
|
| |
|
| Submission date |
Jun 02, 2023 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Joaquin de Navascues Melero |
| E-mail(s) |
j.denavascues@essex.ac.uk
|
| Organization name |
University of Essex
|
| Department |
School of Life Sciences
|
| Street address |
Wivenhoe Park
|
| City |
Colchester |
| State/province |
Essex |
| ZIP/Postal code |
CO4 3SQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE234019 |
Homo- and heterodimerization of bHLH transcription factors balance stemness and bipotential differentiation in the Drosophila adult intestine |
|
| Relations |
| BioSample |
SAMN35574018 |
| SRA |
SRX20581238 |
